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- PDB-3soz: Cytoplasmic Protein STM1381 from Salmonella typhimurium LT2 -

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Basic information

Entry
Database: PDB / ID: 3soz
TitleCytoplasmic Protein STM1381 from Salmonella typhimurium LT2
ComponentsCytoplasmic Protein STM1381Cytoplasm
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Structure and Function of Pathogen Secreted Proteins / Program for the Characterization of Secreted Effector Proteins / PCSEP
Function / homologySTM3548-like / Putative glutamine amidotransferase / Putative glutamine amidotransferase / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Cytoplasmic protein
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsJoachimiak, A. / Duke, N.E.C. / Jedrzejczak, R. / Li, H. / Adkins, J. / Brown, R. / Midwest Center for Structural Genomics (MCSG) / Program for the Characterization of Secreted Effector Proteins (PCSEP)
CitationJournal: To be Published
Title: Cytoplasmic Protein STM1381 from Salmonella typhimurium LT2
Authors: Joachimiak, A. / Duke, N.E.C. / Jedrzejczak, R. / Li, H. / Adkins, J. / Brown, R.
History
DepositionJun 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytoplasmic Protein STM1381
B: Cytoplasmic Protein STM1381
C: Cytoplasmic Protein STM1381
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4446
Polymers84,1683
Non-polymers2763
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-35 kcal/mol
Surface area30110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.387, 92.387, 240.904
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Detailstrimer in asymmetric unit

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Components

#1: Protein Cytoplasmic Protein STM1381 / Cytoplasm / ORF 245 protein


Mass: 28055.889 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: ORF 245, orf245, STM1381 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Z4S4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M Acetate pH 4.5 0.8 M NaH2PO4/1.2 M K2HPO4 (Wizard 2, screen 35), VAPOR DIFFUSION, SITTING DROP, temperature 289.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791827 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2011
Details: Si (111) double crystal monochromator sagitally focussing mirror
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791827 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. all: 33198 / Num. obs: 33198 / Observed criterion σ(I): 3 / Redundancy: 7.6 %
Reflection shellResolution: 2.6→2.62 Å / Num. unique all: 1569

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→86.26 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.904 / SU B: 9.941 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2648 1676 5.1 %RANDOM
Rwork0.19244 ---
obs0.19598 31338 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.948 Å2
Baniso -1Baniso -2Baniso -3
1-2.14 Å20 Å20 Å2
2--2.14 Å20 Å2
3----4.28 Å2
Refinement stepCycle: LAST / Resolution: 2.6→86.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5790 0 18 89 5897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225958
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8741.9488103
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8155732
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.91425.056267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.22215966
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.6691512
X-RAY DIFFRACTIONr_chiral_restr0.120.2894
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214527
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9281.53657
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8125907
X-RAY DIFFRACTIONr_scbond_it2.75932301
X-RAY DIFFRACTIONr_scangle_it4.3984.52196
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.599→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 107 -
Rwork0.253 2292 -
obs--99.63 %

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